The family Geminiviridae includes viruses with a circular single-stranded DNA genome (2.6–5.2 kb) encapsulated in geminated quasi-icosahedral particles [1]. This family is divided into 14 genera based on their genome organization, type of vector, phylogenetic relationships, host range, and nucleotide sequence similarity [1]. Members of the genus Begomovirus have one or two genomic components known as DNA-A and DNA-B, are transmitted by whiteflies of the Bemisia tabaci complex [2, 3], and infect a wide range of cultivated and non-cultivated plants, mainly in tropical and subtropical regions [4].

Several different begomoviruses have been reported in non-cultivated plants of the family Euphorbiaceae [5,6,7,8,9,10,11]. In Cnidoscolus urens, a wild plant found in northeastern Brazil, only two viruses have been reported: cnidoscolus mosaic leaf deformation virus (CnMLDV) [12] and cnidoscolus blistering yellow mosaic virus (CnBYMV) [13]. Here, the molecular characteristics of a new bipartite begomovirus infecting C. urens in Pernambuco, Brazil, are described.

A sample of C. urens showing mild mosaic and leaf deformation symptoms was collected in 2019 in Cabo de Santo Agostinho, Pernambuco State, Brazil (Fig. 1), and total DNA was extracted using the CTAB method [14]. Complete viral genomes were amplified by rolling-circle amplification (RCA) [15], cloned, and sequenced commercially by primer walking (Macrogen Inc., South Korea).

Fig. 1
figure 1

Mild mosaic and leaf deformation in Cnidoscolus urens

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The complete nucleotide sequences of the DNA-A and DNA-B genomic components were assembled using CodonCode Aligner v. 6.0.2 and initially analyzed using the BLASTn algorithm [16] to identify the virus with the highest nucleotide sequence similarity. Pairwise sequence identity comparisons were performed using SDT 1.2 software [17].

Multiple sequence alignments were made using the MUSCLE algorithm implemented in MEGA6 [18]. Phylogenetic analysis was performed on the CIPRES Science Gateway [19] using MrBayes v.3.3.3 [20]. The GTR+I+G model was selected as the best nucleotide substitution model for the DNA-A and DNA-B component datasets. The analysis was carried out using two replicates with four chains each for 10 million generations and sampling every 1000 steps (a total of 10,000 trees). The first 2500 trees were discarded as burn-in. Trees were viewed and edited using Figtree v.1.4

A total of five sequences were obtained: three for the DNA-A component and two for the DNA-B component. The sequence of DNA-A is 2657 nt in length (GenBank accession nos. MZ465527, MZ465586, and MZ465587), and that of DNA-B is 2622 nt in length (MZ465585 and MZ46526). The sequences revealed a typical New World begomovirus gene organization, with DNA-A encoding a coat protein (CP) in the virion-sense strand and a replication-associated protein (Rep), a trans-acting protein (TrAP), a replication enhancer (Ren), AC4, and AC5 in the complementary-sense strand, and with DNA-B encoding two proteins, a nuclear shuttle protein (NSP) in the virion-sense strand and a movement protein (MP) in the complementary-sense strand (Supplementary Table S1). Analysis of the common region (CR) showed a conserved nonanucleotide (5'-TAATATT/AC-3') and three putative iterons (GGGT), one of which was inverted (Supplementary Fig. S1). The CR (200 nt) showed 96% nucleotide sequence identity between the two components, suggesting that they are a cognate pair.

Pairwise comparisons showed that the clones BR_Ca96_19A (MZ465527), BR_Ca112_19A (MZ465586), and BR_Ca113_19A (MZ465587) shared 88.6–88.9% sequence identity with CnMLDV (NC_038982; Supplementary Fig. S2). Based on established criteria for species demarcation within the genus Begomovirus [1], this virus, for which we propose the name "cnidoscolus mild mosaic virus" (CnMMV), should be considered a member of a new species, for which we propose the name "Begomovirus caboniensis", according to the binomial nomenclature system recently established by ICTV [21].

Bayesian inference phylogenetic trees (Fig. 2) were constructed to analyze the DNA-A and DNA-B components. In both trees, the isolates from this study clustered with a CnMLDV isolate (KT966772), confirming their genetic relationship. No evidence of recombination was detected using the RDP 4 program [22].

Fig. 2
figure 2

Phylogenetic analysis of DNA-A (a) and DNA-B (b) of cnidoscolus mild mosaic virus (highlighted in red) and the most closely related begomoviruses. Tomato leaf curl New Delhi virus (ToLCNDV) was used as an outgroup. The phylogenetic trees were constructed using the Bayesian inference method.

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In the present study, a new bipartite begomovirus infecting C. urens was characterized. Host-range and infectivity studies are needed to confirm the potential of C. urens as a virus reservoir.